I think it is much better to stay at Inns and hire a car. The nicer campgrounds might be $35-$60/night off season. The higher amount would be for a 3-way hook up (water, electricity and sewer). The problem with an RV is that you will have to unhook and hook everything back up to do any traveling. This takes time. Some streets are extremely narrow. I would not want to drive an RV into Boothbay Harbor.
We pull a camping trailer and love campgrounds but there are too many narrow streets and small parking lots in New England. It would be ok if you were also towing a car. Some campgrounds have rental trailers or cabins. You might check into those. Late September weather can be glorious or iffy. Friends and I take a long weekend the third weekend in Sept. Recently we have started staying in condos and cooking some of our meals. We stayed at a nice little cottage colony on the Cape the year before last. Check the ferry schedule to MV and where you want to stay. We had to get on the road early in the morning to get to the remote parking lot and buy tickets since we stayed a little too far away. Once on MV you can take a van tour of the island or part of it to get around. We did not use the bus but I understand the service is very good.